library(LEEF.analysis)
library(LEEF.measurement.toc)
library(dplyr)
Attaching package: 'dplyr'The following objects are masked from 'package:stats':
filter, lagThe following objects are masked from 'package:base':
intersect, setdiff, setequal, unionlibrary(tidyr)
library(ggplot2)
library(ggExtra)
options(dplyr.summarise.inform = FALSE)root_folder <- params$root_folder
db <- params$db
options(RRDdb = db)
unlink(file.path(root_folder, "1.pre-processed.data", "toc"))
pre_processor_toc(file.path(root_folder, "0.raw.data"), file.path(root_folder, "1.pre-processed.data"))[1] "Log file set to ~/Desktop//1.pre-processed.data/toc/toc.log"
########################################################
Processing tocdone
########################################################unlink(file.path(root_folder, "2.extracted.data", "toc"))
extractor_toc(file.path(root_folder, "1.pre-processed.data"), file.path(root_folder, "2.extracted.data"))Extracting toc[1] "Log file set to ~/Desktop//2.extracted.data/toc/toc.log"
########################################################Extracting tocProcessing LEEF_ 22_06_17A.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_ 22_06_20A.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_ 22_06_20B.txt ...Warning in readLines(fn): incomplete final line found on
'/Users/rainerkrug/Desktop//1.pre-processed.data/toc/LEEF_ 22_06_20B.txt' |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_21_09_20 und 21_09_22 C.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_21_09_24 1-8.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_21_09_24 und 21_09_27 B.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_21_09_27 restB.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_21_09_29t.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_21_10_01.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_21_10_04 S22 - S30.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_21_10_04 und 21_10_06A.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_21_10_06.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_21_10_08.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_21_10_11.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_21_10_13.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_21_10_15 s8 - 26.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_21_10_15.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_21_10_18.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_21_10_20.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_21_10_22.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_21_10_25.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_21_10_27.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_21_10_29 und 21_11_01.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_21_11_03 und 21_11_05.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_21_11_08 und 21_11_10.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_21_11_12.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_21_11_17 und 21_11_19.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_21_11_22 und 21_11_24.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_21_11_26 und 21_11_29.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_21_12_01 und 21_12_03A.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_21_12_03B.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_21_12_06 und 21_12_08 1-8A.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_21_12_08B.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_21_12_10 und 21_12_13.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_21_12_15 und 21_12_17.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_21_12_20 und 21_12_22.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_21_12_24.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_21_12_27 und 21_12_29.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_21_12_31 und 22_01_03.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_21_15_10 rest 2.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_01_05 und 22_01_07A.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_01_10 und 22_01_12.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_01_14 und 22_01_17.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_01_19 und 22_01_21A.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_01_19 und 22_01_21B.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_01_24 und 22_01_26.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_01_28 und 22_01_31A.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_02_02 und 22_02_04.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_02_07B.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_02_07D.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_02_09 und 22_02_11A.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_02_14 und 22_02_16A.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_02_16B.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_02_18A.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_02_18B.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_02_21A.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_02_23A.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_02_25.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_02_28.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_03_02.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_03_04.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_03_07.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_03_09.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_03_11.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_03_14.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_03_16.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_03_18.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_03_21.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_03_23.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_03_25.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_03_28.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_03_30A.txt ...Warning in readLines(fn): incomplete final line found on
'/Users/rainerkrug/Desktop//1.pre-processed.data/toc/LEEF_22_03_30A.txt' |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_03_30B.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_04_01.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_04_04A.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_04_04B.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_04_06.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_04_08.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_04_11.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_04_13.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_04_15A.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_04_15B.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_04_18.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_04_20.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_04_22.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_04_25.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_04_27.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_04_29.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_05_02.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_05_04.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_05_06.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_05_09.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_05_11.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_05_13.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_05_16.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_05_18.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_05_20.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_05_23A.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_05_25A.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_05_27A.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_05_30A.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_06_01A.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_06_03A.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_06_06A.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_06_08A.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_06_10B.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_06_13A.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_06_15A.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_06_20F.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing calibration ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_06_22A.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing calibration ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_06_27A.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing calibration ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_06_29B.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing calibration ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_07_04A.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing calibration ... |- Processing actual data ... |- Saving files ...done
########################################################fns <- sapply(
list.files(file.path(root_folder, "2.extracted.data", "toc"), "\\.data\\.", full.names = FALSE),
function(fn){
x <- strsplit(fn, "\\.")[[1]][[1]]
}
)
data <- lapply(
fns,
function(fn){
p <- read.csv(file.path(root_folder, "2.extracted.data", "toc", paste(fn, "parameter", "csv", sep = ".")))
d <- read.csv(file.path(root_folder, "2.extracted.data", "toc", paste(fn, "data", "csv", sep = ".")))
return(list(
data = d,
parameter = p,
samples = max(p$samples),
extra_samples = max(p$extra_samples),
max_cv = max(p$max_cv)
)
)
}
)
sapply(data, "[[", "samples") |> plot(ylab = "samples") |> print()
NULLsapply(data, "[[", "extra_samples") |> plot(ylab = "extra_samples") |> print()
NULLsapply(data, "[[", "max_cv") |> plot(ylab = "max_cv") |> print()
NULLsamples <- sapply(data, "[[", "samples") |> min()
extra_samples <- sapply(data, "[[", "extra_samples") |> min()
max_cv <- sapply(data, "[[", "max_cv") |> max()
no_samples <- samples + extra_samples
max_col <- (2 + 3 + no_samples * 2) + 1As the number of additional samples as well as the cv were different for some samples, we have to re-calculate conc and cv. The values which will be used are
In case there are more extra samples, the last ones were be discarded.
toc <- lapply(
data,
function(x){
result <- x$data[,1:max_col]
return(result)
}
) |> do.call(what = rbind)
toc$id <- 1:nrow(toc)inj_typeWe have the following measurements files with measurements without inj_type or NULL. These can nod be analysed and need to be excluded.
toc %>%
filter(inj_type == "") %>%
group_by(filename) %>%
summarise(n = n()) %>%
collect() %>%
knitr::kable()| filename | n |
|---|---|
| LEEF_ 22_06_20A | 78 |
| LEEF_ 22_06_20B | 2 |
| LEEF_21_09_24 1-8 | 208 |
| LEEF_22_01_19 und 22_01_21A | 196 |
| LEEF_22_02_09 und 22_02_11A | 3 |
| LEEF_22_02_14 und 22_02_16A | 3 |
| LEEF_22_02_16B | 3 |
| LEEF_22_04_04A | 54 |
| LEEF_22_04_15A | 58 |
| LEEF_22_06_03A | 6 |
| LEEF_22_06_06A | 6 |
| LEEF_22_06_08A | 6 |
| LEEF_22_06_10B | 6 |
| LEEF_22_06_13A | 6 |
| LEEF_22_06_15A | 6 |
These can be filtered out
before <- nrow(toc)
toc <- toc %>%
filter(inj_type != "")
after <- nrow(toc)
cat("Before : ", before, "\n")Before : 17424 cat("Removed: ", before - after, "\n")Removed: 645 cat("After : ", after, "\n")After : 16779 In addition to the analysed samples, two more validation and null samples (H2O) were taken. Upon further consideration, these were considered as not useful and excluded from the analysis. They are saved as toc_val_samples.csv.
toc %>%
filter(identification == "H2O" | identification == "2.5mg/lIC") %>%
group_by(filename) %>%
summarise(n = n()) %>%
collect() %>%
knitr::kable()| filename | n |
|---|---|
| LEEF_ 22_06_17A | 8 |
| LEEF_ 22_06_20A | 4 |
| LEEF_ 22_06_20B | 4 |
| LEEF_21_09_20 und 21_09_22 C | 16 |
| LEEF_21_09_24 1-8 | 8 |
| LEEF_21_09_24 und 21_09_27 B | 16 |
| LEEF_21_09_27 restB | 16 |
| LEEF_21_09_29t | 16 |
| LEEF_21_10_01 | 16 |
| LEEF_21_10_04 S22 - S30 | 12 |
| LEEF_21_10_04 und 21_10_06A | 16 |
| LEEF_21_10_06 | 16 |
| LEEF_21_10_08 | 16 |
| LEEF_21_10_11 | 16 |
| LEEF_21_10_13 | 8 |
| LEEF_21_10_15 | 8 |
| LEEF_21_10_15 s8 - 26 | 4 |
| LEEF_21_10_18 | 8 |
| LEEF_21_10_20 | 8 |
| LEEF_21_10_22 | 8 |
| LEEF_21_10_25 | 8 |
| LEEF_21_10_27 | 8 |
| LEEF_21_10_29 und 21_11_01 | 12 |
| LEEF_21_11_03 und 21_11_05 | 12 |
| LEEF_21_11_08 und 21_11_10 | 12 |
| LEEF_21_11_12 | 12 |
| LEEF_21_11_17 und 21_11_19 | 12 |
| LEEF_21_11_22 und 21_11_24 | 12 |
| LEEF_21_11_26 und 21_11_29 | 12 |
| LEEF_21_12_01 und 21_12_03A | 12 |
| LEEF_21_12_03B | 8 |
| LEEF_21_12_06 und 21_12_08 1-8A | 12 |
| LEEF_21_12_08B | 4 |
| LEEF_21_12_10 und 21_12_13 | 12 |
| LEEF_21_12_15 und 21_12_17 | 12 |
| LEEF_21_12_20 und 21_12_22 | 12 |
| LEEF_21_12_24 | 8 |
| LEEF_21_12_27 und 21_12_29 | 12 |
| LEEF_21_12_31 und 22_01_03 | 12 |
| LEEF_21_15_10 rest 2 | 4 |
| LEEF_22_01_05 und 22_01_07A | 12 |
| LEEF_22_01_10 und 22_01_12 | 12 |
| LEEF_22_01_14 und 22_01_17 | 12 |
| LEEF_22_01_19 und 22_01_21A | 4 |
| LEEF_22_01_19 und 22_01_21B | 12 |
| LEEF_22_01_24 und 22_01_26 | 12 |
| LEEF_22_01_28 und 22_01_31A | 16 |
| LEEF_22_02_02 und 22_02_04 | 16 |
| LEEF_22_02_07B | 8 |
| LEEF_22_02_07D | 8 |
| LEEF_22_02_09 und 22_02_11A | 13 |
| LEEF_22_02_14 und 22_02_16A | 13 |
| LEEF_22_02_16B | 5 |
| LEEF_22_02_18A | 12 |
| LEEF_22_02_18B | 12 |
| LEEF_22_02_21A | 12 |
| LEEF_22_02_23A | 12 |
| LEEF_22_02_25 | 12 |
| LEEF_22_02_28 | 12 |
| LEEF_22_03_02 | 12 |
| LEEF_22_03_04 | 12 |
| LEEF_22_03_07 | 16 |
| LEEF_22_03_09 | 16 |
| LEEF_22_03_11 | 16 |
| LEEF_22_03_14 | 16 |
| LEEF_22_03_16 | 16 |
| LEEF_22_03_18 | 16 |
| LEEF_22_03_21 | 16 |
| LEEF_22_03_23 | 16 |
| LEEF_22_03_25 | 16 |
| LEEF_22_03_28 | 16 |
| LEEF_22_03_30A | 8 |
| LEEF_22_03_30B | 8 |
| LEEF_22_04_01 | 16 |
| LEEF_22_04_04A | 8 |
| LEEF_22_04_04B | 8 |
| LEEF_22_04_06 | 16 |
| LEEF_22_04_08 | 16 |
| LEEF_22_04_11 | 16 |
| LEEF_22_04_13 | 16 |
| LEEF_22_04_15A | 8 |
| LEEF_22_04_15B | 8 |
| LEEF_22_04_18 | 16 |
| LEEF_22_04_20 | 16 |
| LEEF_22_04_22 | 16 |
| LEEF_22_04_25 | 16 |
| LEEF_22_04_27 | 16 |
| LEEF_22_04_29 | 16 |
| LEEF_22_05_02 | 16 |
| LEEF_22_05_04 | 16 |
| LEEF_22_05_06 | 16 |
| LEEF_22_05_09 | 16 |
| LEEF_22_05_11 | 16 |
| LEEF_22_05_13 | 16 |
| LEEF_22_05_16 | 16 |
| LEEF_22_05_18 | 16 |
| LEEF_22_05_20 | 16 |
| LEEF_22_05_23A | 16 |
| LEEF_22_05_25A | 16 |
| LEEF_22_05_27A | 16 |
| LEEF_22_05_30A | 16 |
| LEEF_22_06_01A | 16 |
| LEEF_22_06_03A | 10 |
| LEEF_22_06_06A | 10 |
| LEEF_22_06_08A | 10 |
| LEEF_22_06_10B | 10 |
| LEEF_22_06_13A | 10 |
| LEEF_22_06_15A | 10 |
| LEEF_22_06_20F | 3 |
| LEEF_22_06_22A | 8 |
| LEEF_22_06_27A | 8 |
| LEEF_22_06_29B | 8 |
| LEEF_22_07_04A | 8 |
These can be filtered out
unlink(file.path(root_folder, "2.extracted.data", "toc_val_samples.csv"))
toc %>%
filter(identification == "H2O" | identification == "2.5mg/lIC") %>%
write.csv(file = file.path(root_folder, "2.extracted.data", "toc_val_samples.csv"))
before <- nrow(toc)
toc <- toc %>%
filter(identification != "H2O" & identification != "2.5mg/lIC")
after <- nrow(toc)
cat("Before : ", before, "\n")Before : 16779 cat("Removed: ", before - after, "\n")Removed: 1374 cat("After : ", after, "\n")After : 15405 In each file, there should be a maximum of 1 timestamp, except of files which contain two timestamps, i.e. which are named accodingly.
toc %>%
select(filename, timestamp, identification, inj_type) %>%
filter(identification != "H2O" & identification != "2.5mg/lIC") %>%
group_by(filename, timestamp) %>%
summarise(timestamps_count = n()) %>%
group_by(filename) %>%
summarise(number_of_timestamps = n()) %>%
arrange(desc(number_of_timestamps)) %>%
knitr::kable()| filename | number_of_timestamps |
|---|---|
| LEEF_21_09_20 und 21_09_22 C | 2 |
| LEEF_21_09_24 und 21_09_27 B | 2 |
| LEEF_21_10_04 und 21_10_06A | 2 |
| LEEF_21_10_29 und 21_11_01 | 2 |
| LEEF_21_11_03 und 21_11_05 | 2 |
| LEEF_21_11_08 und 21_11_10 | 2 |
| LEEF_21_11_12 | 2 |
| LEEF_21_11_17 und 21_11_19 | 2 |
| LEEF_21_11_22 und 21_11_24 | 2 |
| LEEF_21_11_26 und 21_11_29 | 2 |
| LEEF_21_12_01 und 21_12_03A | 2 |
| LEEF_21_12_06 und 21_12_08 1-8A | 2 |
| LEEF_21_12_10 und 21_12_13 | 2 |
| LEEF_21_12_15 und 21_12_17 | 2 |
| LEEF_21_12_20 und 21_12_22 | 2 |
| LEEF_21_12_27 und 21_12_29 | 2 |
| LEEF_21_12_31 und 22_01_03 | 2 |
| LEEF_22_01_05 und 22_01_07A | 2 |
| LEEF_22_01_10 und 22_01_12 | 2 |
| LEEF_22_01_14 und 22_01_17 | 2 |
| LEEF_22_01_19 und 22_01_21B | 2 |
| LEEF_22_01_24 und 22_01_26 | 2 |
| LEEF_22_01_28 und 22_01_31A | 2 |
| LEEF_22_02_02 und 22_02_04 | 2 |
| LEEF_22_02_09 und 22_02_11A | 2 |
| LEEF_22_02_14 und 22_02_16A | 2 |
| LEEF_ 22_06_17A | 1 |
| LEEF_ 22_06_20A | 1 |
| LEEF_ 22_06_20B | 1 |
| LEEF_21_09_24 1-8 | 1 |
| LEEF_21_09_27 restB | 1 |
| LEEF_21_09_29t | 1 |
| LEEF_21_10_01 | 1 |
| LEEF_21_10_04 S22 - S30 | 1 |
| LEEF_21_10_06 | 1 |
| LEEF_21_10_08 | 1 |
| LEEF_21_10_11 | 1 |
| LEEF_21_10_13 | 1 |
| LEEF_21_10_15 | 1 |
| LEEF_21_10_15 s8 - 26 | 1 |
| LEEF_21_10_18 | 1 |
| LEEF_21_10_20 | 1 |
| LEEF_21_10_22 | 1 |
| LEEF_21_10_25 | 1 |
| LEEF_21_10_27 | 1 |
| LEEF_21_12_03B | 1 |
| LEEF_21_12_08B | 1 |
| LEEF_21_12_24 | 1 |
| LEEF_21_15_10 rest 2 | 1 |
| LEEF_22_01_19 und 22_01_21A | 1 |
| LEEF_22_02_07B | 1 |
| LEEF_22_02_07D | 1 |
| LEEF_22_02_16B | 1 |
| LEEF_22_02_18A | 1 |
| LEEF_22_02_18B | 1 |
| LEEF_22_02_21A | 1 |
| LEEF_22_02_23A | 1 |
| LEEF_22_02_25 | 1 |
| LEEF_22_02_28 | 1 |
| LEEF_22_03_02 | 1 |
| LEEF_22_03_04 | 1 |
| LEEF_22_03_07 | 1 |
| LEEF_22_03_09 | 1 |
| LEEF_22_03_11 | 1 |
| LEEF_22_03_14 | 1 |
| LEEF_22_03_16 | 1 |
| LEEF_22_03_18 | 1 |
| LEEF_22_03_21 | 1 |
| LEEF_22_03_23 | 1 |
| LEEF_22_03_25 | 1 |
| LEEF_22_03_28 | 1 |
| LEEF_22_03_30A | 1 |
| LEEF_22_03_30B | 1 |
| LEEF_22_04_01 | 1 |
| LEEF_22_04_04A | 1 |
| LEEF_22_04_04B | 1 |
| LEEF_22_04_06 | 1 |
| LEEF_22_04_08 | 1 |
| LEEF_22_04_11 | 1 |
| LEEF_22_04_13 | 1 |
| LEEF_22_04_15A | 1 |
| LEEF_22_04_15B | 1 |
| LEEF_22_04_18 | 1 |
| LEEF_22_04_20 | 1 |
| LEEF_22_04_22 | 1 |
| LEEF_22_04_25 | 1 |
| LEEF_22_04_27 | 1 |
| LEEF_22_04_29 | 1 |
| LEEF_22_05_02 | 1 |
| LEEF_22_05_04 | 1 |
| LEEF_22_05_06 | 1 |
| LEEF_22_05_09 | 1 |
| LEEF_22_05_11 | 1 |
| LEEF_22_05_13 | 1 |
| LEEF_22_05_16 | 1 |
| LEEF_22_05_18 | 1 |
| LEEF_22_05_20 | 1 |
| LEEF_22_05_23A | 1 |
| LEEF_22_05_25A | 1 |
| LEEF_22_05_27A | 1 |
| LEEF_22_05_30A | 1 |
| LEEF_22_06_01A | 1 |
| LEEF_22_06_03A | 1 |
| LEEF_22_06_06A | 1 |
| LEEF_22_06_08A | 1 |
| LEEF_22_06_10B | 1 |
| LEEF_22_06_13A | 1 |
| LEEF_22_06_15A | 1 |
| LEEF_22_06_20F | 1 |
| LEEF_22_06_22A | 1 |
| LEEF_22_06_27A | 1 |
| LEEF_22_06_29B | 1 |
| LEEF_22_07_04A | 1 |
Fixed the following typos in the raw data. Now, it looks OK for me.
LEEF_21_12_10 und 21_12_13: typos in IdentificationLEEF_22_05_18: typo in IdentificatioLEEF_21_11_12: File name should be LEEF_21_11_12 und 21_15_10ALEEF_22_01_19 und 22_01_21A: All analysis for 22_01_21 are not validNAA density plot of the values of the TC measurements in all measurements.
tc <- toc %>%
filter(inj_type == "TC")
tc <- data.frame(conc_TC = c(tc$conc_1, tc$conc_2, tc$conc_3))
tc %>% ggplot(aes(x=conc_TC)) +
stat_density(bw = 0.1, na.rm = TRUE) +
geom_vline(xintercept = 5, col = "red")
One can see for TC two peaks clearly separated. The values smaller than 5 will be set to NA as they are unrealistically low and can be linked to measuring errors in the machine.
Plot the previous plot zoomed in to conc <= 10 for each bottle
toc %>%
filter(inj_type == "TC") %>%
ggplot(aes(x=conc_1)) +
geom_vline(xintercept = 5, col = "red") +
stat_density(bw = 0.1, na.rm = TRUE) +
facet_wrap(~bottle, ncol = 1, scales = "free_y")Warning: Groups with fewer than two data points have been dropped.Warning: Removed 1 rows containing missing values (`position_stack()`).
toc %>%
filter(inj_type == "TC") %>%
ggplot(aes(x=conc_2)) +
geom_vline(xintercept = 5, col = "red") +
stat_density(bw = 0.1, na.rm = TRUE) +
facet_wrap(~bottle, ncol = 1, scales = "free_y")Warning: Groups with fewer than two data points have been dropped.Warning: Removed 1 rows containing missing values (`position_stack()`).
toc %>%
filter(inj_type == "TC") %>%
ggplot(aes(x=conc_3)) +
geom_vline(xintercept = 5, col = "red") +
stat_density(bw = 0.1, na.rm = TRUE) +
facet_wrap(~bottle, ncol = 1, scales = "free_y")
tc <- (toc$inj_type == "TC")
toc$conc_1[tc & sapply(toc$conc_1 < 5, isTRUE)] <- NA
toc$conc_2[tc & sapply(toc$conc_2 < 5, isTRUE)] <- NA
toc$conc_3[tc & sapply(toc$conc_3 < 5, isTRUE)] <- NAtc <- toc %>%
filter(inj_type == "TC")
tc <- data.frame(conc_TC = c(tc$conc_1, tc$conc_2, tc$conc_3))
tc %>% ggplot(aes(x=conc_TC)) +
stat_density(bw = 0.1, na.rm = TRUE) +
geom_vline(xintercept = 5, col = "red")
NAA density plot of the values of the IC measurements in all measurements.
tc <- toc %>%
filter(inj_type == "IC")
tc <- data.frame(conc_IC = c(tc$conc_1, tc$conc_2, tc$conc_3))
tc %>%
ggplot(aes(x=conc_IC)) +
geom_vline(xintercept = 0.2, col = "red") +
stat_density(bw = 0.001, na.rm = TRUE)
One can see for TC two peaks clearly separated. The values smaller than 0.3 will be set to NA as they are unrealistically low and can be linked to measuring errors in the machine.
Plot the previous plot zoomed in to conc <= 3 for each bottle
toc %>%
filter(inj_type == "IC") %>%
ggplot(aes(x=conc_1)) +
geom_vline(xintercept = 0.2, col = "red") +
stat_density(bw = 0.01, na.rm = TRUE) +
facet_wrap(~bottle, ncol = 1, scales = "free_y")Warning: Groups with fewer than two data points have been dropped.Warning: Removed 1 rows containing missing values (`position_stack()`).
toc %>%
filter(inj_type == "IC") %>%
ggplot(aes(x=conc_2)) +
geom_vline(xintercept = 0.3, col = "red") +
stat_density(bw = 0.01, na.rm = TRUE) +
facet_wrap(~bottle, ncol = 1, scales = "free_y")Warning: Groups with fewer than two data points have been dropped.Warning: Removed 1 rows containing missing values (`position_stack()`).
toc %>%
filter(inj_type == "IC") %>%
ggplot(aes(x=conc_3)) +
geom_vline(xintercept = 0.3, col = "red") +
stat_density(bw = 0.01, na.rm = TRUE) +
facet_wrap(~bottle, ncol = 1, scales = "free_y")
tc <- (toc$inj_type == "IC")
toc$conc_1[tc & sapply(toc$conc_1 < 0.3, isTRUE)] <- NA
toc$conc_2[tc & sapply(toc$conc_2 < 0.3, isTRUE)] <- NA
toc$conc_3[tc & sapply(toc$conc_3 < 0.3, isTRUE)] <- NAtc <- toc %>%
filter(inj_type == "IC")
tc <- data.frame(conc_IC = c(tc$conc_1, tc$conc_2, tc$conc_3))
tc %>% ggplot(aes(x=conc_IC)) +
geom_vline(xintercept = 0.3, col = "red") +
stat_density(bw = 0.001, na.rm = TRUE)
conc and cv for all measurements except TOCAs the number of additional samples as well as the cv were different for some samples, we have to re-calculate conc and cv. The values which will be used are - samples: 2 - extra_samples: 1 - max_cv: 3 In case there are more extra samples, the last ones were be discarded.
As we are re-calculating TOC later, we can exclude the TOC values here.
conc and cvcvf <- function(x, y){
sapply(
1:length(x),
function(i){
sd(c(x[i], y[i])) / mean(c(x[i], y[i])) * 100
}
)
}
toc$cv_12 <- cvf(toc$conc_1, toc$conc_2)
toc$cv_13 <- cvf(toc$conc_1, toc$conc_3)
toc$cv_23 <- cvf(toc$conc_2, toc$conc_3)
toc$conc_12 <- rowMeans(toc[,c("conc_1", "conc_2")])
toc$conc_13 <- rowMeans(toc[,c("conc_1", "conc_3")])
toc$conc_23 <- rowMeans(toc[,c("conc_2", "conc_3")])
for (i in 1:nrow(toc)){
if (toc[i,"inj_type"] == "TOC"){
next()
}
if (isTRUE(as.numeric(toc[i,][["cv_12"]]) < max_cv)) {111
toc[i,]$conc <- mean(as.numeric(toc[i,][["conc_1"]]), as.numeric(toc[i,][["conc_2"]]))
toc[i,]$cv <- as.numeric(toc[i,][["cv_12"]])
} else {
sel <- suppressWarnings(
which(
toc[i, c("cv_12", "cv_13", "cv_23")] == min(
as.numeric(toc[i,][["cv_12"]]),
as.numeric(toc[i,][["cv_13"]]),
as.numeric(toc[i,][["cv_23"]]),
na.rm = TRUE
)
)
)
if (length(sel) == 0) {
toc[i,]$conc <- NA
toc[i,]$cv <- NA
next()
}
if (((as.numeric(toc[i,][c("conc_1", "conc_2", "conc_3")]) == 0) |> sum(na.rm = TRUE)) > 1) {
toc[i,]$conc <- NA
toc[i,]$cv <- NA
next()
}
if (sel == 1) {
toc[i,]$conc <- mean(as.numeric(toc[i,][["conc_1"]]), as.numeric(toc[i,][["conc_2"]]))
toc[i,]$cv <- as.numeric(toc[i,][["cv_12"]])
next()
}
if (sel == 2) {
toc[i,]$conc <- mean(as.numeric(toc[i,][["conc_1"]]), as.numeric(toc[i,][["conc_3"]]))
toc[i,]$cv <- as.numeric(toc[i,][["cv_13"]])
next()
}
if (sel == 3) {
toc[i,]$conc <- mean(as.numeric(toc[i,][["conc_2"]]), as.numeric(toc[i,][["conc_3"]]))
toc[i,]$cv <- as.numeric(toc[i,][["cv_23"]])
next()
} else {
stop("Here is something seriously wrong!!!!")
}
}
}Now we re-calculate the TOC values.
toc$conc[which(toc$inj_type == "TOC")] <- NA
TOC_calc <- toc %>%
mutate(an_id = paste(filename, position)) %>%
pivot_wider(id_cols = an_id, names_from = inj_type, values_from = conc) %>%
mutate(TOC_calc = TC - IC) %>%
select(an_id, TOC_calc) %>%
mutate(an_id = paste(an_id, "TOC"))
toc <- toc %>%
mutate(an_id = paste(filename, position, inj_type)) %>%
left_join(TOC_calc, by = "an_id") %>%
mutate( conc = ifelse(inj_type == "TOC", TOC_calc, conc) ) %>%
select( -TOC_calc, -an_id)toc %>%
ggplot(aes(x=conc)) +
stat_density(bw = 0.1, na.rm = TRUE) +
facet_grid(rows = vars(inj_type), scales = "free_y")
toc %>%
ggplot(aes(x=conc)) +
stat_density(bw = 0.1, na.rm = TRUE) +
facet_grid(rows = vars(bottle), cols = vars(inj_type), scales = "free")Warning: Groups with fewer than two data points have been dropped.
Groups with fewer than two data points have been dropped.
Groups with fewer than two data points have been dropped.
Groups with fewer than two data points have been dropped.Warning: Removed 4 rows containing missing values (`position_stack()`).
toc %>%
filter(inj_type == "TC") %>%
ggplot(aes(x=conc)) +
geom_vline(xintercept = 5, col = "red") +
stat_density(bw = 0.1, na.rm = TRUE) +
facet_wrap(~bottle, ncol = 1, scales = "free_y")Warning: Groups with fewer than two data points have been dropped.Warning: Removed 1 rows containing missing values (`position_stack()`).
toc %>%
filter(inj_type == "IC") %>%
ggplot(aes(x=conc)) +
geom_vline(xintercept = 0.3, col = "red") +
stat_density(bw = 0.01, na.rm = TRUE) +
facet_wrap(~bottle, ncol = 1, scales = "free_y")Warning: Groups with fewer than two data points have been dropped.Warning: Removed 1 rows containing missing values (`position_stack()`).
toc %>%
filter(inj_type == "TOC") %>%
ggplot(aes(x=conc)) +
geom_vline(xintercept = 4.7, col = "red") +
stat_density(bw = 0.1, na.rm = TRUE) +
facet_wrap(~bottle, ncol = 1, scales = "free_y")Warning: Groups with fewer than two data points have been dropped.Warning: Removed 1 rows containing missing values (`position_stack()`).
toc %>%
filter(inj_type == "TN") %>%
ggplot(aes(x=conc)) +
stat_density(bw = 0.1, na.rm = TRUE) +
facet_wrap(~bottle, ncol = 1, scales = "free_y")Warning: Groups with fewer than two data points have been dropped.Warning: Removed 1 rows containing missing values (`position_stack()`).
The toc is now added to the database
add_to_and_overwrite_table_in_RRD(toc = toc, dbname = db)[1] 0toc_original <- toc
toc$id <- 1:nrow(toc)Now let’s look at the plots of the measurements per bottle per timestep
if (params$LEEF == "LEEF_1") {
p1 <- plot_tocs_per_bottle_per_timestamp(db = db, c("TC", "TOC"))
p2 <- plot_tocs_per_bottle_per_timestamp(db = db, c("IC"))
p3 <- plot_tocs_per_bottle_per_timestamp(db = db, c("TN"))
} else {
p1 <- LEEF_2_plot_tocs_per_bottle_per_timestamp(db = db, c("TC", "TOC"))
p2 <- LEEF_2_plot_tocs_per_bottle_per_timestamp(db = db, c("IC"))
p3 <- LEEF_2_plot_tocs_per_bottle_per_timestamp(db = db, c("TN"))
}Warning: Missing values are always removed in SQL aggregation functions.
Use `na.rm = TRUE` to silence this warning
This warning is displayed once every 8 hours.p1
p2
p3
timestamp, bottle and inj_typeWe have to look if there are any duplicate measurements.
dupl <- toc %>%
group_by(timestamp, bottle, inj_type) %>%
filter(!is.na(bottle)) %>%
summarise(fn_1 = min(filename), fn_2 = max(filename), count = n(), min_conc = min(conc), max_conc = max(conc)) %>%
filter(count > 1 & count < 10) %>%
mutate(diff = max_conc - min_conc) %>%
arrange(inj_type, diff)
dupl %>%
group_by(fn_1, fn_2, timestamp) %>%
summarise() %>%
arrange(timestamp) %>%
knitr::kable()| fn_1 | fn_2 | timestamp |
|---|---|---|
| LEEF_21_09_24 1-8 | LEEF_21_09_24 und 21_09_27 B | 20210924 |
| LEEF_21_09_24 und 21_09_27 B | LEEF_21_09_27 restB | 20210927 |
| LEEF_21_10_04 S22 - S30 | LEEF_21_10_04 und 21_10_06A | 20211004 |
| LEEF_21_10_04 und 21_10_06A | LEEF_21_10_06 | 20211006 |
| LEEF_21_10_01 | LEEF_21_10_29 und 21_11_01 | 20211101 |
| LEEF_21_10_15 s8 - 26 | LEEF_21_11_12 | 20211115 |
| LEEF_21_10_15 s8 - 26 | LEEF_21_15_10 rest 2 | 20211115 |
| LEEF_21_12_01 und 21_12_03A | LEEF_21_12_03B | 20211203 |
| LEEF_21_12_06 und 21_12_08 1-8A | LEEF_21_12_08B | 20211208 |
| LEEF_22_01_19 und 22_01_21A | LEEF_22_01_19 und 22_01_21B | 20220119 |
| LEEF_22_02_07B | LEEF_22_02_07D | 20220207 |
| LEEF_22_02_14 und 22_02_16A | LEEF_22_02_16B | 20220216 |
| LEEF_22_02_18A | LEEF_22_02_18B | 20220218 |
| LEEF_22_03_30A | LEEF_22_03_30B | 20220330 |
| LEEF_22_04_04A | LEEF_22_04_04B | 20220404 |
| LEEF_22_04_15A | LEEF_22_04_15B | 20220415 |
| LEEF_ 22_06_20A | LEEF_ 22_06_20B | 20220620 |
And some plots of the duplicate concentration values only
dat <- db_read_toc(db = db, duplicates = NULL) %>%
collect()
if (nrow(dat) > 0){
dat$id <- 1:nrow(dat)
ids <- dat %>%
filter(!is.na(bottle)) %>%
group_by(timestamp, bottle, type) %>%
summarize(min(id), max(id), n = n()) %>%
filter(n > 1)
ids <- c(ids$`min(id)`, ids$`max(id)`) |>
unique()
x <- dat %>%
filter(id %in% ids) %>%
group_by(day, timestamp, bottle, type) %>%
summarise(timestamp, bottle, type, mic = min(concentration), mac = max(concentration)) %>%
mutate(mdiff = mac - mic)
}if (nrow(x) > 0){
pl <- x %>%
filter(type == "TN") %>%
ggplot2::ggplot(ggplot2::aes(x = mic, y = mac, colour = type)) +
ggplot2::geom_point() +
ggplot2::xlab("Smaler concentration Value") +
ggplot2::ylab("Larger concentration Value")
ggMarginal(pl, type="histogram")
}Warning: Removed 308 rows containing missing values (`geom_point()`).
if (nrow(x) > 0){
pl <- x %>%
filter(type == "TC") %>%
ggplot2::ggplot(ggplot2::aes(x = mic, y = mac, colour = type)) +
ggplot2::geom_point() +
ggplot2::xlab("Smaler concentration Value") +
ggplot2::ylab("Larger concentration Value")
ggMarginal(pl, type="histogram")
}Warning: Removed 306 rows containing missing values (`geom_point()`).
if (nrow(x) > 0){
pl <- x %>%
filter(type == "IC") %>%
ggplot2::ggplot(ggplot2::aes(x = mic, y = mac, colour = type)) +
ggplot2::geom_point() +
ggplot2::xlab("Smaler concentration Value") +
ggplot2::ylab("Larger concentration Value")
ggMarginal(pl, type="histogram")
}Warning: Removed 316 rows containing missing values (`geom_point()`).
if (nrow(x) > 0){
pl <- x %>%
filter(type == "TOC") %>%
ggplot2::ggplot(ggplot2::aes(x = mic, y = mac, colour = type)) +
ggplot2::geom_point() +
ggplot2::xlab("Smaler concentration Value") +
ggplot2::ylab("Larger concentration Value")
ggMarginal(pl, type="histogram")
}Warning: Removed 318 rows containing missing values (`geom_point()`).
try(
report_diagnostic(
db = params$db,
template = params$LEEF,
suffix = "TOC_added",
format = "html"
)
)
processing file: DiagnosticReport.RmdError in parse_block(g[-1], g[1], params.src, markdown_mode) :
Duplicate chunk label 'setup', which has been used for the chunk:
library(LEEF.analysis)
library(LEEF.measurement.toc)
library(dplyr)
library(tidyr)
library(ggplot2)
library(ggExtra)
options(dplyr.summarise.inform = FALSE)